Misfire/drop in performance over 3500rpm

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Mazdaspeed Protege
So I bought my car, drove it a bit and performance wasn't great, AND I was having a problem where sometimes when I go to start it, it won't start, I turn the key and.. Nothing. Parked it after a few days because it needed new suspension and brakes, and CEL came on with codes:
P0302 missfire cyl 2
P0704 Clutch switch failure
P0660 Secondary Shutter Valve Open

I replaced the wires, coils and plugs.
I replaced the clutch switch
Replaced the VICS.

I replaced the suspension and brakes, took it for a test drive and everything seemed fine, but the next day, I couldn't get it to start again for nothing, I put the battery on the charger thinking maybe I had drained the battery a bit too far (though all the lights and everything had turned on) And after that it still took a number of tries to get it to engage the starter motor, I can hear it "click" but it doesn't engage the motor until I've depressed the clutch a number of times. I noticed that the clutch switch is wired into the engine bay, some hack job. I'll try to get better pictures, but its weird. (a lot of the wiring is, since the PO did a big hack job of getting t an after market radio in there).

but I also still have that missfire/it bogs down, and sometimes won't rev over 4000 rpm. CEL hasn't come back on yet, but what else could I look at to see what might cause the missfire. Its really frustrating.
 
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